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LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma
  1. Jiagen Li1,
  2. Zhaoli Chen1,
  3. Liqing Tian2,
  4. Chengcheng Zhou1,
  5. Max Yifan He1,
  6. Yibo Gao1,
  7. Suya Wang1,
  8. Fang Zhou1,
  9. Susheng Shi3,
  10. Xiaoli Feng3,
  11. Nan Sun1,
  12. Ziyuan Liu1,
  13. Geir Skogerboe2,
  14. Jingsi Dong1,
  15. Ran Yao1,
  16. Yuda Zhao1,
  17. Jian Sun1,
  18. Baihua Zhang1,
  19. Yue Yu1,
  20. Xuejiao Shi1,
  21. Mei Luo1,
  22. Kang Shao1,
  23. Ning Li1,
  24. Bin Qiu1,
  25. Fengwei Tan1,
  26. Runsheng Chen2,
  27. Jie He1
  1. 1Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
  2. 2Bioinformatics Laboratory and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, The People's Republic of China
  3. 3Department of Pathology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The People's Republic of China
  1. Correspondence to Dr Jie He, Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Panjiayuannanli No 17, Chaoyang District, Beijing 10021, The People's Republic of China; prof.hejie{at}gmail.com and Runsheng Chen, Bioinformatics Laboratory and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Datun Rd No. 15, Chaoyang District, Beijing, 100101, The People's Republic of China; crs{at}sun5.ibp.ac.cn

Abstract

Background Oesophageal cancer is one of the most deadly forms of cancer worldwide. Long non-coding RNAs (lncRNAs) are often found to have important regulatory roles.

Objective To assess the lncRNA expression profile of oesophageal squamous cell carcinoma (OSCC) and identify prognosis-related lncRNAs.

Method LncRNA expression profiles were studied by microarray in paired tumour and normal tissues from 119 patients with OSCC and validated by qRT-PCR. The 119 patients were divided randomly into training (n=60) and test (n=59) groups. A prognostic signature was developed from the training group using a random Forest supervised classification algorithm and a nearest shrunken centroid algorithm, then validated in a test group and further, in an independent cohort (n=60). The independence of the signature in survival prediction was evaluated by multivariable Cox regression analysis.

Results LncRNAs showed significantly altered expression in OSCC tissues. From the training group, we identified a three-lncRNA signature (including the lncRNAs ENST00000435885.1, XLOC_013014 and ENST00000547963.1) which classified the patients into two groups with significantly different overall survival (median survival 19.2 months vs >60 months, p<0.0001). The signature was applied to the test group (median survival 21.5 months vs >60 months, p=0.0030) and independent cohort (median survival 25.8 months vs >48 months, p=0.0187) and showed similar prognostic values in both. Multivariable Cox regression analysis showed that the signature was an independent prognostic factor for patients with OSCC. Stratified analysis suggested that the signature was prognostic within clinical stages.

Conclusions Our results suggest that the three-lncRNA signature is a new biomarker for the prognosis of patients with OSCC, enabling more accurate prediction of survival.

  • Oesophageal Cancer

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/3.0/

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